6NMM | pdb_00006nmm

Ternary complex structure of the T130K mutant of ANT-4 with Neomycin, AMPCPP and Pyrophosphate

PDB DOI: https://doi.org/10.2210/pdb6NMM/pdb

Classification: transferase/ANTIBIOTIC
Organism(s): Geobacillus stearothermophilus
Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
Mutation(s): No

Deposited: 2019-01-11 Released: 2020-01-15
Deposition Author(s): Cuneo, M.J., Selvaraj, B.
Funding Organization(s): National Science Foundation (NSF, United States), Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.230 (Depositor), 0.233 (DCC)
R-Value Work:
0.174 (Depositor)
R-Value Observed:
0.176 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

'Catch and Release": a Variation of the Archetypal Nucleotidyl Transfer Reaction

Selvaraj, B., Kocaman, S., Trifas, M., Serpersu, E.H., Cuneo, M.J.

(2020) ACS Catal

DOI: https://doi.org/10.1021/acscatal.9b05201

Macromolecule Content

Total Structure Weight: 123.22 kDa
Atom Count: 8,755
Modeled Residue Count: 1,008
Deposited Residue Count: 1,024
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kanamycin nucleotidyltransferase	A, B, C, D	256	Geobacillus stearothermophilus	Mutation(s): 0 EC: 2.7.7
UniProt
Find proteins for P05057 (Staphylococcus aureus) Explore P05057 Go to UniProtKB: P05057
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05057
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NMY Query on NMY Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain Q [auth C] SDF format, chain X [auth D] SDF format, chain V [auth C] SDF format, chain E [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain X [auth D] MOL2 format, chain V [auth C] MOL2 format, chain E [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain X [auth D] mmCIF format, chain V [auth C] mmCIF format, chain E [auth A]	E [auth A] J [auth A] L [auth B] Q [auth C] V [auth C] E [auth A], J [auth A], L [auth B], Q [auth C], V [auth C], X [auth D]	NEOMYCIN C₂₃ H₄₆ N₆ O₁₃ PGBHMTALBVVCIT-VCIWKGPPSA-N		Interactions Focus chain E [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain V [auth C] Focus chain X [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain V [auth C] Focus chain X [auth D]
AMP Query on AMP Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain W [auth C] SDF format, chain Y [auth D] SDF format, chain R [auth C] SDF format, chain M [auth B] SDF format, chain F [auth A] MOL2 format, chain K [auth A] MOL2 format, chain W [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain R [auth C] MOL2 format, chain M [auth B] MOL2 format, chain F [auth A] mmCIF format, chain K [auth A] mmCIF format, chain W [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain R [auth C] mmCIF format, chain M [auth B] mmCIF format, chain F [auth A]	F [auth A] K [auth A] M [auth B] R [auth C] W [auth C] F [auth A], K [auth A], M [auth B], R [auth C], W [auth C], Y [auth D]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain W [auth C] Focus chain Y [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain W [auth C] Focus chain Y [auth D]
PPV Query on PPV Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth B] SDF format, chain Z [auth D] SDF format, chain S [auth C] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Z [auth D] MOL2 format, chain S [auth C] mmCIF format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain Z [auth D] mmCIF format, chain S [auth C]	G [auth A], N [auth B], S [auth C], Z [auth D]	PYROPHOSPHATE H₄ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain N [auth B] Focus chain S [auth C] Focus chain Z [auth D] Interactions & Density Focus chain G [auth A] Focus chain N [auth B] Focus chain S [auth C] Focus chain Z [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth D] H [auth A] I [auth A] O [auth B] AA [auth D], BA [auth D], H [auth A], I [auth A], O [auth B], P [auth B], T [auth C], U [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.230 (Depositor), 0.233 (DCC)
R-Value Work: 0.174 (Depositor)
R-Value Observed: 0.176 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.51	α = 90
b = 59.25	β = 94.8
c = 102.04	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-01-15

Deposition Author(s):

Cuneo, M.J.

Selvaraj, B.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	--
Department of Energy (DOE, United States)	United States	--

Revision History (Full details and data files)

Version 1.0: 2020-01-15
Type: Initial release
Version 1.1: 2020-01-29
Changes: Database references
Version 1.2: 2020-02-26
Changes: Database references
Version 1.3: 2020-05-06
Changes: Database references
Version 1.4: 2024-03-13
Changes: Data collection, Database references, Derived calculations
Version 2.0: 2024-05-29
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-12-25
Changes: Advisory, Derived calculations, Structure summary